Genotyping Microarrays

For most researchers DNA microarrays are synonymous with high-throughput gene expression analysis. But they also are invaluable genotyping tools. Now that the International HapMap Project (see article, p.68) is complete companies are putting ?these tools into researchers hands, including the HumanHap300 BeadChip from San Diego-based Illumina, whose construction is illustrated here.

Unlike other microarray platforms, in which specific oligonucleotide probes are either synthesized in situ or spotted onto the array in a particular, predefined arrangement, each Illumina BeadArray is unique. (1) Individual beads that have been coupled to hundreds of thousands of oligos (each bearing the same sequence) are pooled and randomly assembled into a slide-shaped device called a BeadChip (2). The company uses a decoding process (3) to map the location of each bead, creating a BeadMap file for the end user. Armed with that file, the user can then map hybridization signals to individual polymorphisms, producing a genome-scale...